a) Composition and functions of fecal microbiota

Composition

• Bacteria, which are the dominant and best-characterized component. The principal phyla are:
  • Firmicutes (including many butyrate-producing organisms)
  • Bacteroidetes/Bacteroidota
  • Actinobacteria
  • Proteobacteria
• Archaea, especially methanogens such as Methanobrevibacter.
• Viruses, chiefly bacteriophages, which regulate bacterial populations.
• Fungi and yeasts, the mycobiome.
• Small amounts of protozoal and other eukaryotic genetic material.

Functions

1. Metabolic and nutritional functions
   • Fermentation of otherwise indigestible dietary fiber and resistant starch.
   • Production of short-chain fatty acids (SCFAs), especially butyrate, acetate, and propionate. Butyrate is an important fuel for colonocytes and supports epithelial integrity.
   • Synthesis or contribution to availability of vitamins, notably vitamin K and some B vitamins.
   • Metabolism of bile acids, amino acids, xenobiotics, and drugs.
   • Salvage of energy from food residues.
2. Colonization resistance
   • Suppresses pathogens by competing for nutrients and epithelial attachment sites.
   • Produces antimicrobial metabolites and modifies the luminal environment.
   • Converts primary to secondary bile acids, helping inhibit Clostridioides difficile spore germination and growth. Antibiotics disrupt this ecological protection.
3. Barrier maintenance
   • Promotes mucus production, epithelial renewal, tight-junction function, and gut barrier integrity.
   • Helps limit translocation of microbes and microbial products across the intestinal wall.
4. Immune development and regulation
   • Shapes mucosal immune maturation, including IgA responses and regulatory T-cell activity.
   • Maintains a controlled balance between tolerance of commensals and defense against pathogens.
5. Systemic signaling
   • Microbial metabolites influence metabolism, hepatic function, inflammation, and gut-brain signaling. Associations with obesity, inflammatory bowel disease, colorectal cancer, and neuropsychiatric disorders are being studied, but association does not by itself prove causation.

b) Fecal microbiota transplantation: definition, indications, and contraindications

Definition

Current accepted clinical indications

1. Recurrent Clostridioides difficile infection (rCDI)

• Immunocompetent adults with recurrent CDI
• Mildly to moderately immunocompromised adults with recurrent CDI, using conventional FMT selectively
• Adults hospitalized with severe or fulminant CDI not responding to standard antimicrobial therapy, where conventional FMT may be used selectively as adjunctive rescue therapy

• REBYOTA: rectally administered fecal microbiota, live-jslm
• VOWST: orally administered fecal microbiota spores, live-brpk

2. Other uses: investigational, not routine clinical indications

• Ulcerative colitis
• Crohn disease
• Pouchitis
• Irritable bowel syndrome
• Hepatic encephalopathy
• Metabolic disease and obesity
• Multidrug-resistant organism decolonization
• Cancer immunotherapy modulation

Contraindications and situations requiring avoidance

A. Do not use unscreened or inadequately screened donor material

• Enteric pathogens, including toxigenic C. difficile
• Multidrug-resistant organisms
• Hepatitis viruses, HIV, and other blood-borne infections
• SARS-CoV-2 or other emerging infection risks, according to current local protocols
• Relevant travel, antimicrobial use, high-risk behavior, gastrointestinal disease, metabolic disease, and malignancy history

B. Severe immunocompromise

C. Contraindications related to the route or procedure

• Suspected or established intestinal perforation
• Peritonitis
• Bowel obstruction or severe ileus, depending on route
• Toxic megacolon, if colonoscopy would be unsafe
• Severe hemodynamic or cardiopulmonary instability that makes endoscopy or sedation unsafe
• High aspiration risk for nasogastric, nasoduodenal, or oral delivery

D. Other cautions

• Informed consent is essential because conventional FMT can transmit known or unknown infectious, metabolic, or immune-mediated risks.
• Use particular caution in pregnancy, pediatrics, advanced cirrhosis, frailty, and serious comorbidity, because evidence is less secure.
• Confirm that ongoing diarrhea is truly due to active CDI rather than colonization or another cause before proceeding.

c) FMT techniques and future perspectives

Core steps in conventional FMT

1. Donor selection and screening
   • Healthy volunteer donors are selected through questionnaires, examination, blood testing, and stool testing.
   • Stool banks can provide standardized screened preparations where available.
2. Recipient preparation
   • Confirm active/recurrent CDI clinically and microbiologically.
   • Treat the acute episode with guideline-based antibiotics.
   • Antibiotics are usually stopped shortly before FMT according to local protocol.
   • Bowel preparation is often used when colonoscopic delivery is planned.
3. Stool processing
   • Stool is mixed with sterile saline or another diluent, homogenized, filtered to remove particulate material, and administered fresh or stored frozen.
   • Modern products may be concentrated, purified, spore-based, lyophilized, or encapsulated.
   • Standardized manufacturing aims to reduce donor-to-donor variability.

Routes of administration

Adverse effects

• Bloating, abdominal cramps, nausea, flatulence
• Loose stools or transient constipation
• Low-grade fever or fatigue

• Transmitted bacterial, viral, or parasitic infections
• Bacteremia or sepsis, especially in high-risk recipients
• Aspiration with upper-GI delivery
• Colonoscopy-related complications
• Possible transfer of poorly understood long-term metabolic, immune, or antimicrobial-resistance traits

Future perspectives of fecal microbiota therapy

1. Move from donor stool to defined products
   Future therapy is likely to rely increasingly on standardized, quality-controlled microbial consortia rather than heterogeneous whole stool. These may contain selected live strains, spores, metabolites, or bacteriophages.
2. Precision microbiota treatment
   Donor-recipient matching and baseline metagenomic profiling may help identify which patient needs which microbial function, rather than using a one-size-fits-all transplant.
3. Defined microbial consortia and next-generation probiotics
   Cultured mixtures of known organisms may restore key functions such as butyrate production, bile-acid conversion, or resistance to C. difficile, while reducing infection-transmission risk.
4. Bacteriophage and targeted antimicrobial approaches
   Phages may selectively suppress pathogenic or antibiotic-resistant bacteria without broadly disturbing beneficial organisms. Bacteriophages can shape intestinal bacterial communities and are a potential therapeutic platform. Sleisenger and Fordtran's Gastrointestinal and Liver Disease, p. 53.
5. Non-bacterial microbiome components
   Future interventions may account for fungi, bacteriophages, viruses, and their interactions with bacteria and host immunity, not bacteria alone.
6. Better regulation and long-term surveillance
   Major needs include harmonized donor screening, validated manufacturing standards, product traceability, registries for delayed adverse effects, and long-term outcome data.
7. Expansion beyond CDI only after high-quality trials
   UC, IBS, metabolic disease, hepatic encephalopathy, and oncology remain active research areas. At present, promising findings should not be mistaken for established routine therapy. Current guideline-based practice remains focused on selected recurrent, severe, or fulminant CDI scenarios.